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<i>Raoultella ornithinolytica</i> is an <i>Enterobacteriaceae</i> bacterium that can infect both humans and animals, while luteolin-7-O-glucoside (IOG) is a flavonoid that has broad effects on the intestinal microbiota of healthy animals. However, current studies lack sufficient data on intestinal microbiota dysbiosis and drug resistance transmission caused by <i>R. ornithinolytica</i> and the possible role of IOG. In this study, BALB/c mice were infected with <i>R. ornithinolytica</i> carrying <i>bla</i>_NDM-1 gene and treated with IOG (3 mg/kg·d and 6 mg/kg·d) to analyze the diversity of intestinal microbiota and the transfer of <i>bla</i>_NDM-1 between bacteria. The findings indicated that <i>R. ornithinolytica</i> B1645-1 exhibited a significant ability to enhance the <i>Firmicutes</i>/<i>Bacteroidota</i> ratio and increase the relative abundance of <i>Lactobacillus</i> and <i>Bacillus</i> after 48 h, where as 6 mg/kg·d IOG had an opposite effect. Moreover, <i>R. ornithinolytica</i> B1645-1 facilitated the emergence of drug-resistant bacteria and promoted <i>bla</i>_NDM-1 gene transfer in <i>Enterococcus</i>, <i>Escherichia</i>, <i>Klebsiella</i>, <i>Acinetobacter</i>, <i>Bacillus</i>, <i>Brevibacterium</i>, and <i>Lactobacillus</i>. <i>Enterococcus</i> was the predominant genus at 48 h. Surprisingly, 6 mg/kg·d IOG significantly inhibited the production of drug-resistant bacteria and promoted <i>bla</i>_NDM-1 gene transfer from <i>Enterococcus</i> to <i>Lactobacillus</i> at 144 h. However, the role of <i>Lactobacillus</i> as a recipient for drug-resistant genes should be of more concern.